Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

ES Lander, 2001, Initial sequencing and analysis of the human genome., Nature, 409, 860, 10.1038/35057062

FCO Roudier, 2011, Integrative epigenomic mapping defines four main chromatin states in Arabidopsis., EMBO J, 30, 1928, 10.1038/emboj.2011.103

RK Slotkin, 2007, Transposable elements and the epigenetic regulation of the genome., Nat Rev Genet, 8, 272, 10.1038/nrg2072

Z Lippman, 2004, Role of transposable elements in heterochromatin and epigenetic control., Nature, 430, 471, 10.1038/nature02651

F-L Sun, 2004, cis-Acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four., Mol Cell Biol, 24, 8210, 10.1128/MCB.24.18.8210-8220.2004

AA Aravin, 2008, A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice., Mol Cell, 31, 785, 10.1016/j.molcel.2008.09.003

JA Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals., Nat Rev Genet

ER Havecker, 2010, The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci., Plant Cell, 22, 321, 10.1105/tpc.109.072199

V Pereira, 2004, Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome., Genome Biol, 5, R79, 10.1186/gb-2004-5-10-r79

DA Wright, 1998, Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins., Genetics, 149, 703, 10.1093/genetics/149.2.703

A Steimer, 2000, Endogenous targets of transcriptional gene silencing in Arabidopsis., Plant Cell, 12, 1165, 10.1105/tpc.12.7.1165

RK Slotkin, 2009, Epigenetic reprogramming and small RNA silencing of transposable elements in pollen., Cell, 136, 461, 10.1016/j.cell.2008.12.038

R Lister, 2008, Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis., Cell, 133, 523, 10.1016/j.cell.2008.03.029

Z Lippman, 2003, Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification., PLoS Biol, 1, e67, 10.1371/journal.pbio.0000067

M Mirouze, 2009, Selective epigenetic control of retrotransposition in Arabidopsis., Nature, 461, 427, 10.1038/nature08328

M Tanurdzic, 2008, Epigenomic consequences of immortalized plant cell suspension culture., PLoS Biol, 6, e302, 10.1371/journal.pbio.0060302

B Czech, 2011, Small RNA sorting: matchmaking for Argonautes., Nat Rev Genet, 12, 19, 10.1038/nrg2916

C Rouget, 2010, Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo., Nature, 467, 1128, 10.1038/nature09465

T Watanabe, 2011, Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus., Science, 332, 848, 10.1126/science.1203919

NA Smith, 2011, Viral small interfering RNAs target host genes to mediate disease symptoms in plants., PLoS Pathog, 7, e1002022, 10.1371/journal.ppat.1002022

Z Xie, 2004, Genetic and functional diversification of small RNA pathways in plants., PLoS Biol, 2, e104, 10.1371/journal.pbio.0020104

P Dunoyer, 2010, An endogenous, systemic RNAi pathway in plants., EMBO J, 29, 1699, 10.1038/emboj.2010.65

EJ Chapman, 2007, Specialization and evolution of endogenous small RNA pathways., Nat Rev Genet, 8, 884, 10.1038/nrg2179

P Dunoyer, 2005, DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal., Nat Genet, 37, 1356, 10.1038/ng1675

F Schwach, 2005, An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal., Plant Physiol, 138, 1842, 10.1104/pp.105.063537

A Deleris, 2006, Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense., Science, 313, 68, 10.1126/science.1128214

H Garcia-Ruiz, 2010, Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection., Plant Cell, 22, 481, 10.1105/tpc.109.073056

P Dunoyer, 2010, Small RNA duplexes function as mobile silencing signals between plant cells., Science, 328, 912, 10.1126/science.1185880

M Arteaga-Vázquez, 2006, A family of microRNAs present in plants and animals., Plant Cell, 18, 3355, 10.1105/tpc.106.044420

NL Kedersha, 1999, RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules., J Cell Biol, 147, 1431, 10.1083/jcb.147.7.1431

C Weber, 2008, Plant stress granules and mRNA processing bodies are distinct from heat stress granules., Plant J, 56, 517, 10.1111/j.1365-313X.2008.03623.x

BC Meyers, 2008, Criteria for annotation of plant MicroRNAs., Plant Cell, 20, 3186, 10.1105/tpc.108.064311

M Nakano, 2006, Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA., Nucleic Acids Res, 34, D731, 10.1093/nar/gkj077

L Johnson, 2002, Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation., Curr Biol, 12, 1360, 10.1016/S0960-9822(02)00976-4

H Hirochika, 2000, Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation., Plant Cell, 12, 357, 10.1105/tpc.12.3.357

T Kakutani, 1996, Developmental abnormalities and epimutations associated with DNA hypomethylation mutations., Proc Natl Acad Sci USA, 93, 12406, 10.1073/pnas.93.22.12406

S Boutet, 2003, Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance., Curr Biol, 13, 843, 10.1016/S0960-9822(03)00293-8

T Kanno, 2005, Atypical RNA polymerase subunits required for RNA-directed DNA methylation., Nat Genet, 37, 761, 10.1038/ng1580

V Gasciolli, 2005, Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs., Curr Biol, 15, 1494, 10.1016/j.cub.2005.07.024

A Vongs, 1993, Arabidopsis thaliana DNA methylation mutants., Science, 260, 1926, 10.1126/science.8316832

T Kakutani, 1999, Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana., Genetics, 151, 831, 10.1093/genetics/151.2.831

FK Teixeira, 2009, A role for RNAi in the selective correction of DNA methylation defects., Science, 323, 1600, 10.1126/science.1165313

D Didiano, 2006, Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions., Nat Struct Mol Biol, 13, 849, 10.1038/nsmb1138

R Schwab, 2006, Highly specific gene silencing by artificial microRNAs in Arabidopsis., Plant Cell, 18, 1121, 10.1105/tpc.105.039834

Z Luo, 2007, Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis., Plant Cell, 19, 943, 10.1105/tpc.106.045724

J Liu, 2008, Control of protein synthesis and mRNA degradation by microRNAs., Curr Opin Cell Biol, 20, 214, 10.1016/j.ceb.2008.01.006

C Addo-Quaye, 2008, Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome., Curr Biol, 18, 758, 10.1016/j.cub.2008.04.042

MA German, 2008, Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends., Nat Biotechnol, 26, 941, 10.1038/nbt1417

AD McCue, 2011, Cytoplasmic connection of sperm cells to the pollen vegetative cell nucleus: potential roles of the male germ unit revisited., J Exp Bot, 62, 1621, 10.1093/jxb/err032

F Borges, 2008, Comparative transcriptomics of Arabidopsis sperm cells., Plant Physiol, 148, 1168, 10.1104/pp.108.125229

N Baumberger, 2005, Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs., Proc Natl Acad Sci USA, 102, 11928, 10.1073/pnas.0505461102

H Wang, 2011, Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions., Plant J, 67, 292, 10.1111/j.1365-313X.2011.04594.x

M Piecyk, 2000, TIA-1 is a translational silencer that selectively regulates the expression of TNF-alpha., EMBO J, 19, 4154, 10.1093/emboj/19.15.4154

TSK Eisinger-Mathason, 2008, Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival., Mol Cell, 31, 722, 10.1016/j.molcel.2008.06.025

T Zou, 2011, SMN deficiency reduces cellular ability to form stress granules, sensitizing cells to stress., Cell Mol Neurobiol, 31, 541, 10.1007/s10571-011-9647-8

N Gilks, 2004, Stress granule assembly is mediated by prion-like aggregation of TIA-1., Mol Biol Cell, 15, 5383, 10.1091/mbc.E04-08-0715

JR Buchan, 2009, Eukaryotic stress granules: the ins and outs of translation., Mol Cell, 36, 932, 10.1016/j.molcel.2009.11.020

CJ Beckham, 2008, P bodies, stress granules, and viral life cycles., Cell Host Microbe, 3, 206, 10.1016/j.chom.2008.03.004

N Kedersha, 2000, Dynamic shuttling of TIA-1 accompanies the recruitment of mRNA to mammalian stress granules., J Cell Biol, 151, 1257, 10.1083/jcb.151.6.1257

A-V Gendrel, 2002, Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1., Science, 297, 1871, 10.1126/science.1074950

DA Wright, 2002, Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses., Genome Res, 12, 122, 10.1101/gr.196001

RK Slotkin, 2010, The epigenetic control of the Athila family of retrotransposons in Arabidopsis., Epigenetics, 5, 483, 10.4161/epi.5.6.12119

O Borsani, 2005, Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis., Cell, 123, 1279, 10.1016/j.cell.2005.11.035

M Ron, 2010, Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis., Genes Dev, 24, 1010, 10.1101/gad.1882810

X Song, 2011, Roles of DCL4 and DCL3b in Rice Phased Small RNA Biogenesis., Plant J

JT Cuperus, 2010, Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis., Nat Struct Mol Biol, 17, 997, 10.1038/nsmb.1866

A Miura, 2001, Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis., Nature, 411, 212, 10.1038/35075612

M-A Grandbastien, 2004, Stress activation and genomic impact of plant retrotransposons., J Soc Biol, 198, 425, 10.1051/jbio/2004198040425

A Beauregard, 2008, The take and give between retrotransposable elements and their hosts., Annu Rev Genet, 42, 587, 10.1146/annurev.genet.42.110807.091549

O Aparicio, 2010, Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair., Nucleic Acids Res, 38, 750, 10.1093/nar/gkp1028

JP White, 2007, Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase., Cell Host Microbe, 2, 295, 10.1016/j.chom.2007.08.006

A Esclatine, 2004, Herpes simplex virus 1 induces cytoplasmic accumulation of TIA-1/TIAR and both synthesis and cytoplasmic accumulation of tristetraprolin, two cellular proteins that bind and destabilize AU-rich RNAs., J Virol, 78, 8582, 10.1128/JVI.78.16.8582-8592.2004

JL Goodier, 2007, LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex., Mol Cell Biol, 27, 6469, 10.1128/MCB.00332-07

F Vazquez, 2004, Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs., Mol Cell, 16, 69, 10.1016/j.molcel.2004.09.028

TA Montgomery, 2008, AGO1-miR173 complex initiates phased siRNA formation in plants., Proc Natl Acad Sci USA, 105, 20055, 10.1073/pnas.0810241105

G Hutvágner, 2008, Argonaute proteins: key players in RNA silencing., Nature Reviews Molecular Cell Biology, 9, 22, 10.1038/nrm2321

S Mi, 2008, Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide., Cell, 133, 116, 10.1016/j.cell.2008.02.034

A Grundhoff, 2011, Virus-encoded microRNAs., Virology, 411, 325, 10.1016/j.virol.2011.01.002

GS Pall, 2007, Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot., Nucleic Acids Res, 35, e60, 10.1093/nar/gkm112

RK Slotkin, 2005, Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication., Nat Genet, 37, 641, 10.1038/ng1576

V Sundaresan, 1995, Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements., Genes Dev, 9, 1797, 10.1101/gad.9.14.1797

RA Jefferson, 1987, Assaying Chimeric Genes in Plants: The GUS Gene Fusion System., Plant Molecular Biology Reporter, 5, 387, 10.1007/BF02667740

D Twell, 1990, Pollen-specific gene expression in transgenic plants: coordinate regulation of two different tomato gene promoters during microsporogenesis., Development, 109, 705, 10.1242/dev.109.3.705

N Baumberger, 2007, The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation., Curr Biol, 17, 1609, 10.1016/j.cub.2007.08.039

CA Kidner, 2004, Spatially restricted microRNA directs leaf polarity through ARGONAUTE1., Nature, 428, 81, 10.1038/nature02366